Question: Viral Encoded miRNA prediction and target identification
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gravatar for micro32uvas
2.9 years ago by
micro32uvas10
Pakistan
micro32uvas10 wrote:

Hi Everybody,

Can anyone help me in prediction viral encoded miRNAs. I have already tried VmiR, Mirna Fold, Mature Bayes for the prediction and then the mature sequence extraction. But I cannot find the targets for them, now, there might be something that I am missing. What can i do for its target prediction in cattle.

Awaiting your responses!

Qurat

ADD COMMENTlink modified 16 months ago by kirrubiosciences0 • written 2.9 years ago by micro32uvas10

Are the viral miRNAs sequence homologuous to some known bovine miRNAs ? If yes you could first check the target of their homologs. You could also use miRanda to predict targets : http://www.microrna.org/microrna/getDownloads.do. Be aware that a LOT of false positives targets will be predicted... Could you precise which virus you are studying ?

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by Nicolas Rosewick8.6k

Well the virus is Bovine viral diarrhea and no I couldn't find homologs for the predicted precursors not with less then 4 mismatches. MiRanda doesn't include cow in the web interface. I am newbie, could you help me in that, #NicoBxl ?

ADD REPLYlink written 2.9 years ago by micro32uvas10

You can download a stand alone version of Miranda (unix command' line) and give him as input the mirna sequences and the bovine cDNA sequences (you can find them on ensembl)

ADD REPLYlink written 2.9 years ago by Nicolas Rosewick8.6k

Check out RepTar It has precalculated predicted interactions between viral miRNA and human targets. The algorithm first predict targets and then finds a matching miRNA so it might be useful for predicting viral miRNAs as well, see their paper.

ADD REPLYlink written 2.9 years ago by Asaf6.6k

I was just checking out RepTar, the issue with this one, is its model organism, i.e. only human and mouse. My concern are cow and virus. Infact my target is to find the target genes in the cow. Awaiting your answers :/

ADD REPLYlink written 2.9 years ago by micro32uvas10
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